Variant report

Variant	rs7091958
Chromosome Location	chr10:116438317-116438318
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:116432264..116434343-chr10:116438175..116440004,2	MCF-7	breast:
2	chr10:116425468..116427951-chr10:116436410..116438514,2	MCF-7	breast:
3	chr10:116438066..116439847-chr10:116442150..116444383,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000099204	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11196844	0.83[YRI][hapmap]
rs11196845	1.00[ASW][hapmap];1.00[LWK][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes]
rs11196853	0.92[YRI][hapmap]
rs11196858	1.00[AFR][1000 genomes]
rs11196861	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11196866	1.00[ASN][1000 genomes]
rs11196868	1.00[ASN][1000 genomes]
rs11196869	1.00[CEU][hapmap]
rs11196870	1.00[ASN][1000 genomes]
rs11196871	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196880	1.00[ASN][1000 genomes]
rs12782152	1.00[ASN][1000 genomes]
rs217190	1.00[CEU][hapmap]
rs217191	1.00[CEU][hapmap]
rs217193	1.00[ASN][1000 genomes]
rs217195	1.00[ASN][1000 genomes]
rs217196	1.00[ASN][1000 genomes]
rs217197	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037308	chr10:116141946-116519765	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv540780	chr10:116141946-116519765	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	esv3435429	chr10:116394152-117006347	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7091958	GFRA1	cis	cerebellum	SCAN
rs7091958	RPL13AP6	cis	parietal	SCAN
rs7091958	PDZD8	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116408600-116441400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr10:116424200-116443000	Weak transcription	Esophagus	oesophagus
3	chr10:116425400-116441400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr10:116427600-116438600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr10:116429800-116438600	Weak transcription	Brain Anterior Caudate	brain
6	chr10:116431600-116444000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr10:116432400-116441600	Weak transcription	Fetal Intestine Small	intestine
8	chr10:116433800-116440200	Weak transcription	Lung	lung
9	chr10:116434000-116440200	Weak transcription	Right Atrium	heart
10	chr10:116434200-116441600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr10:116435000-116444000	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr10:116435600-116441400	Weak transcription	Fetal Intestine Large	intestine
13	chr10:116437200-116439400	Enhancers	Fetal Lung	lung
14	chr10:116437400-116440000	Weak transcription	Left Ventricle	heart
15	chr10:116437400-116440200	Weak transcription	Right Ventricle	heart
16	chr10:116437600-116438600	Enhancers	A549	lung
17	chr10:116437600-116439400	Enhancers	Fetal Heart	heart
18	chr10:116437800-116439200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr10:116438000-116438600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr10:116438000-116438800	Enhancers	Pancreatic Islets	Pancreatic Islet
21	chr10:116438000-116439000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr10:116438200-116438400	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr10:116438200-116438400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr10:116438200-116438600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr10:116438200-116438600	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr10:116438200-116438800	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr10:116438200-116438800	Enhancers	Liver	Liver
28	chr10:116438200-116439000	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr10:116438200-116439000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr10:116438200-116439000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr10:116438200-116439000	Enhancers	Stomach Mucosa	stomach
32	chr10:116438200-116439200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr10:116438200-116439200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr10:116438200-116439200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr10:116438200-116439400	Enhancers	Adipose Nuclei	Adipose

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